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Archive for the ‘PubMed’ Category

What’s New for 2013 MeSH for Rare Diseases

MeSH uploaded the disease portion of the Online Mendelian Inheritance in Man (OMIM) database available in the Unified Medical Language System. OMIM is a database that catalogues human diseases with genetic components. Although OMIM disease names are available for searches in PubMed, it is often difficult to index and search for the articles on rare diseases with genetic components due to multiple synonyms used by different scientists that often do not overlap. As was done with NIH Office of Rare Diseases and Research (ORDR) disease terms in 2010, OMIM terms were compared to the existing MeSH descriptors and SCR records. When matches were found, OMIM thesaurus tags were added to the matched MeSH record terms. Where there were no string matches, new disease SCRs were created and mapped to descriptor(s) using the Heading Mapped to (HM) field. MeSH created 3,774 new disease SCRs, and identified and tagged 1,498 existing ORDR SCRs as rare diseases with genetic components during the OMIM load. All OMIM disease names therefore will be available starting with MeSH 2013 for indexers and searchers. The use of the HM field in the disease SCRs will lead to more consistent indexing and retrieval for rare genetic diseases.

There were 2,165 terms in 772 descriptors (MeSH headings) matching OMIM terms and therefore, tagged with the Thesaursus ID (TH)=OMIM (2013). An additional 10,286 terms in 5,453 total SCRs (6,331 terms in 3,774 new SCRs and 3,955 terms in 1,498 existing SCRs) were identified during the load. All newly created SCRs were reviewed and mapped to at least one disease descriptor.

The NLM Technical Bulletin article, What’s New for 2013 MeSH, includes additional information on the OMIM tagging. The NLM Technical Bulletin article, What’s New for 2010 MeSH®, has additional information on the 2010 ORDR term merger into the MeSH vocabulary.

The PubReader View: A New Way to Read Articles in PMC

Full PubReader screen showing first page of an article with the journal banner.In order to keep pace with the continuing advances in web technology, PMC has launched PubReader, an alternative web presentation that offers another, more reader-friendly view of the articles in the PMC archive. Designed particularly for enhancing the readability of PMC journal articles on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers.

Like a printed paper, PubReader breaks an article into multiple columns and pages to improve readability and navigation. PubReader can expand a page to whatever fits on your screen — with multiple columns on a desktop monitor or a single column page on a small tablet. It will even switch to two columns if you rotate the tablet to a landscape view. When you adjust the font size or change the size of the browser window, page boundaries and columns are adjusted automatically.

PubReader can be activated by selecting the PubReader Format in the right-hand column of individual PMC articles. Additional information can be found in the NLM Technical Bulletin and the PubReader About webpage.

PubMed® for Trainers at UCLA

Do you train others to use PubMed? If so, join us for PubMed for Trainers, a hybrid class with three online sessions and one in-person session. The class is eligible for 15 MLA CE credits. The class is an in-depth look at PubMed and a chance to share training ideas with your fellow participants.

More details about the PubMed for Trainers course and registration in Los Angeles is available! This course is taught by trainers from the  National Library of Medicine Training Center (NTC).

National Library of Medicine ALTBIB Portal Gets Refreshed!

NLM’s ALTBIB portal has been updated. ALTBIB provides access to PubMed/MEDLINE citations relevant to alternatives to the use of live vertebrates in biomedical research and testing. Many of the citations provide access to free full text of the article. The site’s topics and subtopics are aligned with current approaches. For example, information is provided on in silico, in vitro, and improved (refined) animal testing methods. Strategies which incorporate validated methods and other approaches are also covered.

ALTBIB also provides access to animal alternatives news sources, such as the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM). The portal has an extensive collection of links to key organizations providing information on alternatives to animal testing. ALTBIB provides access to ICCVAM’s “International Acceptance of Alternative Methods, 1998-2012” and “U.S. and International Milestones in Alternative Test Method Development and Evaluations.”

In addition to the topic area PubMed searches, the ALTBIB portal includes a searchable bibliographic collection on alternatives to animal testing. This collection provides citations from published articles, books, book chapters, and technical reports published from 1980 to 2000. The bibliography features citations concerning methods, tests, assays, and procedures that may prove useful in establishing alternatives to the use of intact vertebrates. The ALTBIB bibliographic collection has not been updated since 2001, when the preformulated searches of PubMed were substituted for collecting a formal bibliography.

PubMed for Handhelds App Available!

PubMed for Handhelds (PubMed4Hh) app is now available for free in the iTunes store.

This is an alternative to saving the PubMed for Handhelds web site as a mobile site. Remember to check out the NLM Gallery of Mobile Apps and Sites to see what’s newly listed!

UK PubMed Central Update

The European Research Council (ERC) announced today that it will participate in the UK PubMed Central (UKPMC) open access repository service, joining 18 existing UK and European funders. The ERC becomes the third European funder to join UKPMC, following Telethon Italy and the Austrian Research Fund.

As a result of this participation, the existing funders have agreed that the service will be rebranded as ‘Europe PubMed Central’ (Europe PMC) by November 1, 2012. A key aim of this initiative is to extend the repository further and encourage other European funders of life sciences research to make the outputs of the research they fund freely available through Europe PMC.

For more information see the announcement from the Wellcome Trust. NLM’s PMC team deserves a lot of credit for UKPMC to expand like this. It speaks to both the quality of the underlying software and the manner in which PMC has worked with the partner sites to ensure their integrity.

New Features for My Bibliography and eRA Commons Users!

The My Bibliography Award View display, a tool developed by NCBI to assist eRA Commons users to comply with the NIH Public Access policy and associate their publications to NIH awards, will be enhanced in the following three ways:

  • eRA Commons account holders will be able to associate any grant with citations in their My Bibliography collection, and they will be able to search for awards with the assistance of auto-complete;
  • eRA users’ My Bibliography collection will be automatically updated to include citations that have been associated to the grants awarded to them;
  • New filter options will be added for paper-grant associations.

Complete details, with associated screen shots, are published in the NLM Technical Bulletin.

PubMed Discovery Tools (Results by Year, PMC Images Search) Added!

Mouseover for the PubMed PubMed “Results by year” and PubMed Central “PMC images search” tools now display in the discovery column for all PubMed users.

The “Results by year” timeline tool displays with search results of 10,000 or more citations. Mousing over the bars in the timeline will show the number of citations for each year. Click the right and left arrows to display older or newer years, and click the individual bars in the timeline to display the results for a single year.

The “PMC images search” tool displays for PubMed search results that meet a number of criteria, e.g., results with a minimum of 250 citations, filters are not active, the search does not include Boolean operators, the search retrieves a minimum of 4 relevant images calculated using a term weighted algorithm.

For additional information, please visit the NLM Technical Bulletin.

NLM Theater Presentations and PowerPoint Presentations from MLA 2012

The Annual Meeting of the Medical Library Association (MLA) was held May 18-23, 2012 at the Washington State Convention Center in Seattle, WA. Attendees were invited to visit the NLM exhibit booth to meet NLM staff and see NLM Web products and services. The NLM Theater at the booth featured demonstrations and tutorials on a wide variety of topics. Recordings of the NLM Theater Presentations are now available:

In addition, the PowerPoint presentations from the NLM Online Users’ Meeting, NLM Update, and DOCLINE Users’ Group Meeting are also available online.

“Branching Out: The MeSH Vocabulary” Video Updated

Branching Out: The MeSH VocabularyBranching Out: The MeSH Vocabulary is an introduction to the development, structure and use of the MeSH vocabulary. The video may be of particular interest to searchers of MEDLINE/PubMed, and is used in the PubMed search classes offered by NLM and the National Training Center and Clearinghouse. This 11-minute video has been updated to include new 2012 screenshots of PubMed and MeSH. Branching Out is also available in m4v format for iOS devices and as a text transcript.